A dahlia in full bloom. Scientists estimate the total number of flowering plant species around the world to be around 400,000. Photograph: Harish Tyagi/EPA

More than 600,000 plant species have been deleted from the dictionary of life after the most comprehensive assessment carried out by scientists.

For centuries, botanists from different parts of the world have been collecting and naming "new" plants without realising that many were in fact the same. The humble tomato boasts 790 different names, for example, while there are 600 different monikers for the oak tree and its varieties.

The result was a list of more than 1 million flowering plant species. Although experts have long known that it included many duplicates, no one was sure how many. Later this year, the study team, led by UK and US scientists, will announce that the real number of flowering plant species around the world is closer to 400,000.

The project - which has taken nearly three years - was the number one request made by the 193 government members of the Convention on Biological Diversity at their meeting in 2002. There were concerns that without this work, it would be impossible to work out how many plants were under threat and how successful conservationists were in saving them.

The information will also be vital for any organisation or researcher looking at "economically important" plants, such as those for food and nutrition or medicine, said Alan Paton, assistant keeper of the herbarium at the Royal Botanic Gardens at Kew, west London, one of the four leading partners in the project.

"On average, one plant might have between two and three names, which doesn't sound a great deal, but if you're trying to find information on a plant, you might not find all [of it] because you're only looking at one name," Paton said. "That's even more critical for economically useful plants: because they are more used, they tend to have more names."

In one example, researchers calculated that for the six most-used species of Plectranthus, a relative of the basil plant, a researcher would miss 80% of information available if they looked under only the most commonly used name. On another database, they found only 150 of 500 nutritionally important plant species using the names cited in current literature.

"By going for one name, we missed the majority of information mankind knows about that plant, which isn't too clever," said Paton. "What's really a breakthrough is we have a place which allows people to search through all the names used."

Kew Gardens joined up nearly three years ago with Missouri Botanical Garden in the US, and experts on two of the biggest and most valuable plant families: legumes, or peas and beans, and Compositae, which includeasters, daisies and sunflowers.

They have since attempted to search existing plant lists and work out an "accepted" name for each species, and then list all known variations. One of the databases was originally set up using £250 left in the will of Charles Darwin. The full results will not be published until the end of the year, but so far the researchers have found 301,000 accepted species, 480,000 alternative names, and have 240,000 left to assess.

Although work will continue to assess smaller plant groups in more detail and check for missed duplications, Paton said they now believe that the true number of plant species will turn out to be "400,000 or just over".

"You can't give an absolute number of names, but we have narrowed the possibility," he said. Previous estimates, without the help of a full assessment, put the figure at between 250,000-400,000.

Most of the work of the study group was sifting and sorting different names allocated to one species, often because scientists were simply not aware of the work of rivals and colleagues who had previously "described" the plant in a scientific journal, or because of confusion caused by superficial differences such as different sized leaves in different climates. In some cases, plants thought to be the same have also been judged to be different species because of differences which have been revealed by later scientific discoveries, such as DNA.

As well as the likely 400,000-odd flowering plants, there are thought to be 15,000 species of ferns and their allies, 1,000 gymnosperms such as conifers, and 23,000 mosses and allies making up the plant kingdom. For comparison there are more than 1 million species of insects listed by science, 28,000 living species of fish, 10,000 birds and 5,400 mammals.